Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2
Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, Couloux A, Coutinho PM, Vries RP de, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier J-M, Quévillon E, Sharon A, Simon A, Have A ten, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun M-H, Dickman M (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS genetics 7(8):e1002230. doi: 10.1371/journal.pgen.1002230
Balkunde R, Pesch M, Hülskamp M (2010) Trichome Patterning in Arabidopsis thaliana. In: Plant Development, vol 91. Elsevier, pp 299–321
Behla R, Hirani AH, Zelmer CD, Yu F, Fernando WGD, McVetty P, Li G (2017) Identification of common QTL for resistance to Sclerotinia sclerotiorum in three doubled haploid populations of Brassica napus (L.). Euphytica 213(11):88. doi: 10.1007/s10681-017-2047-5
Benjamini Y, Hochberg Y (1995) Controlling the False Discovery Rate. A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society: Series B (Methodological) 57(1):289–300. doi: 10.1111/j.2517-6161.1995.tb02031.x
Boland GJ, Hall R (1994) Index of plant hosts of Sclerotinia sclerotiorum. Canadian Journal of Plant Pathology 16(2):93–108. doi: 10.1080/07060669409500766
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic. A flexible trimmer for Illumina sequence data. Bioinformatics (Oxford, England) 30(15):2114–2120. doi: 10.1093/bioinformatics/btu170
Bolser D, Staines DM, Pritchard E, Kersey P (2016) Ensembl Plants. Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data. Methods in molecular biology (Clifton, N.J.) 1374:115–140. doi: 10.1007/978-1-4939-3167-5_6
Bolton MD, Thomma BPHJ, Nelson BD (2006) Sclerotinia sclerotiorum (Lib.) de Bary. Biology and molecular traits of a cosmopolitan pathogen. Molecular plant pathology 7(1):1–16. doi: 10.1111/j.1364-3703.2005.00316.x
Broekgaarden C, Caarls L, Vos IA, Pieterse CMJ, van Wees SCM (2015) Ethylene. Traffic Controller on Hormonal Crossroads to Defense. Plant physiology 169(4):2371–2379. doi: 10.1104/pp.15.01020
Broman KW, Sen S (2009) A Guide to QTL Mapping with R/qtl. Statistics for Biology and Health. Springer-Verlag New York, New York, NY
Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl. QTL mapping in experimental crosses. Bioinformatics (Oxford, England) 19(7):889–890. doi: 10.1093/bioinformatics/btg112
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+. Architecture and applications. BMC bioinformatics 10:421. doi: 10.1186/1471-2105-10-421
Chen H-F, Wang H, Li Z-Y (2007) Production and genetic analysis of partial hybrids in intertribal crosses between Brassica species (B. rapa, B. napus) and Capsella bursa-pastoris. Plant cell reports 26(10):1791–1800. doi: 10.1007/s00299-007-0392-x
Derbyshire M, Denton-Giles M, Hegedus D, Seifbarghy S, Rollins J, van Kan J, Seidl MF, Faino L, Mbengue M, Navaud O, Raffaele S, Hammond-Kosack K, Heard S, Oliver R (2017) The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome biology and evolution. doi: 10.1093/gbe/evx030
Derbyshire MC, Denton-Giles M (2016) The control of sclerotinia stem rot on oilseed rape (Brassica napus ). Current practices and future opportunities. Plant Pathol 65(6):859–877. doi: 10.1111/ppa.12517
Ding Y, Mei J, Chai Y, Yu Y, Shao C, Wu Q, Disi JO, Li Y, Wan H, Qian W (2019b) Simultaneous Transcriptome Analysis of Host and Pathogen Highlights the Interaction Between Brassica oleracea and Sclerotinia sclerotiorum. Phytopathology 109(4):542–550. doi: 10.1094/PHYTO-06-18-0204-R
Ding Y, Mei J, Wu Q, Xiong Z, Li Y, Shao C, Wang L, Qian W (2019a) Synchronous improvement of subgenomes in allopolyploid. A case of Sclerotinia resistance improvement in Brassica napus. Mol Breeding 39(1):1. doi: 10.1007/s11032-018-0915-x
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer ELL, Hirsh L, Paladin L, Piovesan D, Tosatto SCE, Finn RD (2019) The Pfam protein families database in 2019. Nucleic acids research 47(D1):D427-D432. doi: 10.1093/nar/gky995
Fernández-Bautista N, Domínguez-Núñez J, Moreno MM, Berrocal-Lobo M (2016) Plant Tissue Trypan Blue Staining During Phytopathogen Infection. BIO-PROTOCOL 6(24). doi: 10.21769/BioProtoc.2078
Garg H, Atri C, Sandhu PS, Kaur B, Renton M, Banga SK, Singh H, Singh C, Barbetti MJ, Banga SS (2010) High level of resistance to Sclerotinia sclerotiorum in introgression lines derived from hybridization between wild crucifers and the crop Brassica species B. napus and B. juncea. Field Crops Research 117(1):51–58. doi: 10.1016/j.fcr.2010.01.013
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology 29(7):644–652. doi: 10.1038/nbt.1883
Gu Z, Eils R, Schlesner M (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics (Oxford, England) 32(18):2847–2849. doi: 10.1093/bioinformatics/btw313
Gyawali S, Harrington M, Durkin J, Horner K, Parkin IAP, Hegedus DD, Bekkaoui D, Buchwaldt L (2016) Microsatellite markers used for genome-wide association mapping of partial resistance to Sclerotinia sclerotiorum in a world collection of Brassica napus. Mol Breeding 36:72. doi: 10.1007/s11032-016-0496-5
Hauser M-T (2014) Molecular basis of natural variation and environmental control of trichome patterning. Frontiers in plant science 5:320. doi: 10.3389/fpls.2014.00320
Hothorn T, Bretz F, Westfall P (2008) Simultaneous inference in general parametric models. Biometrical journal. Biometrische Zeitschrift 50(3):346–363. doi: 10.1002/bimj.200810425
Hülskamp M, Miséra S, Jürgens G (1994) Genetic dissection of trichome cell development in Arabidopsis. Cell 76(3):555–566. doi: 10.1016/0092-8674(94)90118-x
Joshi RK, Megha S, Rahman MH, Basu U, Kav NNV (2016) A global study of transcriptome dynamics in canola (Brassica napus L.) responsive to Sclerotinia sclerotiorum infection using RNA-Seq. Gene 590(1):57–67. doi: 10.1016/j.gene.2016.06.003
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL (2019) Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature biotechnology 37(8):907–915. doi: 10.1038/s41587-019-0201-4
Li B, Dewey CN (2011) RSEM. Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics 12:323. doi: 10.1186/1471-2105-12-323
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England) 25(16):2078–2079. doi: 10.1093/bioinformatics/btp352
Li J, Zhao Z, Hayward A, Cheng H, Fu D (2015) Integration analysis of quantitative trait loci for resistance to Sclerotinia sclerotiorum in Brassica napus. Euphytica 205(2):483–489. doi: 10.1007/s10681-015-1417-0
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology 15(12):550. doi: 10.1186/s13059-014-0550-8
Mei J, Ding Y, Lu K, Wei D, Liu Y, Disi JO, Li J, Liu L, Liu S, McKay J, Qian W (2013) Identification of genomic regions involved in resistance against Sclerotinia sclerotiorum from wild Brassica oleracea. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 126(2):549–556. doi: 10.1007/s00122-012-2000-x
Mei J, Liu Y, Wei D, Wittkop B, Ding Y, Li Q, Li J, Wan H, Li Z, Ge X, Frauen M, Snowdon RJ, Qian W, Friedt W (2015) Transfer of sclerotinia resistance from wild relative of Brassica oleracea into Brassica napus using a hexaploidy step. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 128(4):639–644. doi: 10.1007/s00122-015-2459-3
Mei J, Qian L, Disi JO, Yang X, Li Q, Li J, Frauen M, Cai D, Qian W (2011) Identification of resistant sources against Sclerotinia sclerotiorum in Brassica species with emphasis on B. oleracea. Euphytica 177(3):393–399. doi: 10.1007/s10681-010-0274-0
Mei J, Shao C, Yang R, Feng Y, Gao Y, Ding Y, Li J, Qian W (2020) Introgression and pyramiding of genetic loci from wild Brassica oleracea into B. napus for improving Sclerotinia resistance of rapeseed. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 133(4):1313–1319. doi: 10.1007/s00122-020-03552-w
Mei J, Wang J, Li Y, Tian S, Wei D, Shao C, Si J, Xiong Q, Li J, Qian W (2017) Mapping of genetic locus for leaf trichome in Brassica oleracea. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 130(9):1953–1959. doi: 10.1007/s00122-017-2936-y
Nayidu NK, Kagale S, Taheri A, Withana-Gamage TS, Parkin IAP, Sharpe AG, Gruber MY, Schiefelbein J (2014b) Comparison of Five Major Trichome Regulatory Genes in Brassica villosa with Orthologues within the Brassicaceae. PloS one 9(4):e95877. doi: 10.1371/journal.pone.0095877
Nayidu NK, Tan Y, Taheri A, Li X, Bjorndahl TC, Nowak J, Wishart DS, Hegedus D, Gruber MY (2014a) Brassica villosa, a system for studying non-glandular trichomes and genes in the Brassicas. Plant molecular biology 85(4-5):519–539. doi: 10.1007/s11103-014-0201-1
Parkin IAP, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL, Denoeud F, Belcram H, Links MG, Just J, Clarke C, Bender T, Huebert T, Mason AS, Pires JC, Barker G, Moore J, Walley PG, Manoli S, Batley J, Edwards D, Nelson MN, Wang X, Paterson AH, King G, Bancroft I, Chalhoub B, Sharpe AG (2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome biology 15(6):R77. doi: 10.1186/gb-2014-15-6-r77
Pertea G, Pertea M (2020) GFF Utilities. GffRead and GffCompare. F1000Research 9. doi: 10.12688/f1000research.23297.2
Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature protocols 11(9):1650–1667. doi: 10.1038/nprot.2016.095
Pertea M, Pertea GM, Antonescu CM, Chang T-C, Mendell JT, Salzberg SL (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature biotechnology 33(3):290–295. doi: 10.1038/nbt.3122
Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic acids research 29(9):e45. doi: 10.1093/nar/29.9.e45
Pinheiro J, Bates D, DebRoy S, Sarkar D (2020) nlme. Linear and nonlinear mixed effects models. https://CRAN.R-project.org/package=nlme
Pré M, Atallah M, Champion A, Vos M de, Pieterse CMJ, Memelink J (2008) The AP2/ERF domain transcription factor ORA59 integrates jasmonic acid and ethylene signals in plant defense. Plant physiology 147(3):1347–1357. doi: 10.1104/pp.108.117523
Quinlan AR, Hall IM (2010) BEDTools. A flexible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England) 26(6):841–842. doi: 10.1093/bioinformatics/btq033
R Core Team (2019) R: A language and environment for statistical computing, Vienna, Austria
Rogers SO, Bendich AJ (1985) Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant molecular biology 5(2):69–76. doi: 10.1007/BF00020088
Taylor A, Coventry E, Jones JE, Clarkson JP (2015) Resistance to a highly aggressive isolate of Sclerotinia sclerotiorum in a Brassica napus diversity set. Plant Pathol 64(4):932–940. doi: 10.1111/ppa.12327
Taylor A, Rana K, Handy C, Clarkson JP (2018) Resistance to Sclerotinia sclerotiorum in wild Brassica species and the importance of Sclerotinia subarctica as a Brassica pathogen. Plant Pathol 67(2):433–444. doi: 10.1111/ppa.12745
The Uniprot Consortium (2019) UniProt. A worldwide hub of protein knowledge. Nucleic acids research 47(D1):D506-D515. doi: 10.1093/nar/gky1049
Uloth MB, You MP, Finnegan PM, Banga SS, Banga SK, Sandhu PS, Yi H, Salisbury PA, Barbetti MJ (2013) New sources of resistance to Sclerotinia sclerotiorum for crucifer crops. Field Crops Research 154:40–52. doi: 10.1016/j.fcr.2013.07.013
Vos IA, Moritz L, Pieterse CMJ, van Wees SCM (2015) Impact of hormonal crosstalk on plant resistance and fitness under multi-attacker conditions. Front. Plant Sci. 6:639. doi: 10.3389/fpls.2015.00639
Wang H, Liu G, Zheng Y, Wang X, Yang Q (2004) Breeding of the Brassica napus cultivar Zhongshuang 9 with high-resistance to Sclerotinia sclerotiorum and dynamics of its important defense enzyme activity. Scientia Agriculutra Sinica 37:23–28
Wang Y, Hou Y-P, Chen C-J, Zhou M-G (2014) Detection of resistance in Sclerotinia sclerotiorum to carbendazim and dimethachlon in Jiangsu Province of China. Australasian Plant Pathol. 43(3):307–312. doi: 10.1007/s13313-014-0271-1
Wei D, Mei J, Fu Y, Disi JO, Li J, Qian W (2014) Quantitative trait loci analyses for resistance to Sclerotinia sclerotiorum and flowering time in Brassica napus. Mol Breeding 34(4):1797–1804. doi: 10.1007/s11032-014-0139-7
Wei L, Jian H, Lu K, Filardo F, Yin N, Liu L, Qu C, Li W, Du H, Li J (2016) Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus. Plant biotechnology journal 14(6):1368–1380. doi: 10.1111/pbi.12501
Wickham H (2016) ggplot2. Elegant graphics for data analysis. Use R! Springer, Cham
Wickham H, François R, Henry L, Müller K (2019) dplyr. A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr
Wu J, Cai G, Tu J, Li L, Liu S, Luo X, Zhou L, Fan C, Zhou Y (2013) Identification of QTLs for resistance to sclerotinia stem rot and BnaC.IGMT5.a as a candidate gene of the major resistant QTL SRC6 in Brassica napus. PloS one 8(7):e67740. doi: 10.1371/journal.pone.0067740
Wu J, Zhao Q, Liu S, Shahid M, Lan L, Cai G, Zhang C, Fan C, Wang Y, Zhou Y (2016) Genome-wide Association Study Identifies New Loci for Resistance to Sclerotinia Stem Rot in Brassica napus. Frontiers in plant science 7:1418. doi: 10.3389/fpls.2016.01418
Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li C-Y, Wei L (2011) KOBAS 2.0. A web server for annotation and identification of enriched pathways and diseases. Nucleic acids research 39(Web Server issue):W316-22. doi: 10.1093/nar/gkr483
Yin X, Yi B, Chen W, Zhang W, Tu J, Fernando WGD, Fu T (2010) Mapping of QTLs detected in a Brassica napus DH population for resistance to Sclerotinia sclerotiorum in multiple environments. Euphytica 173(1):25–35. doi: 10.1007/s10681-009-0095-1
You MP, Uloth MB, Li XX, Banga SS, Banga SK, Barbetti MJ (2016) Valuable New Resistances Ensure Improved Management of Sclerotinia Stem Rot (Sclerotinia sclerotiorum ) in Horticultural and Oilseed Brassica Species. J Phytopathol 164(5):291–299. doi: 10.1111/jph.12456
Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq. Accounting for selection bias. Genome biology 11(2):R14. doi: 10.1186/gb-2010-11-2-r14
Zhao J, Meng J (2003) Genetic analysis of loci associated with partial resistance to Sclerotinia sclerotiorum in rapeseed (Brassica napus L.). TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 106(4):759–764. doi: 10.1007/s00122-002-1171-2
Zhao J, Peltier AJ, Meng J, Osborn TC, Grau CR (2004) Evaluation of Sclerotinia Stem Rot Resistance in Oilseed Brassica napus Using a Petiole Inoculation Technique Under Greenhouse Conditions. Plant disease 88(9):1033–1039. doi: 10.1094/PDIS.2004.88.9.1033
Zhao J, Udall JA, Quijada PA, Grau CR, Meng J, Osborn TC (2006) Quantitative trait loci for resistance to Sclerotinia sclerotiorum and its association with a homeologous non-reciprocal transposition in Brassica napus L. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 112(3):509–516. doi: 10.1007/s00122-005-0154-5
Zhou F, Zhang X-L, Li J-L, Zhu F-X (2014) Dimethachlon Resistance in Sclerotinia sclerotiorum in China. Plant disease 98(9):1221–1226. doi: 10.1094/PDIS-10-13-1072-RE